Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
1
vote
12
replies
2.4k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma
highthroughputassays
R
updated 3 months ago by
Mary
• 0 • written 2.5 years ago by
Ming
▴ 380
0
votes
11
replies
3.8k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate
minfi
updated 3 months ago by
Tim Peters
▴ 180 • written 7.1 years ago by
Jenny Drnevich
★ 2.0k
0
votes
11
replies
1.3k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
luis.franco
• 0
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 9 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 3 months ago by
Guido Hooiveld
★ 4.0k • written 3.3 years ago by
Alberto
• 0
2
votes
11
replies
958
views
Error MakeOrgPackagefromNCBI
Bioconductor
updated 3 months ago by
Guido Hooiveld
★ 4.0k • written 7 months ago by
cinzia.spagnoli
• 0
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 9 months ago by
Erika
• 0 • written 9.3 years ago by
c.lieftink@nki.nl
▴ 40
6
votes
11
replies
1.1k
views
Packages don't update, but no error or warning is thrown
Bioconductor
3 months ago • updated 12 weeks ago
gernophil
• 0
0
votes
11
replies
764
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 10 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
mico
• 0
0
votes
11
replies
2.1k
views
globaltest question
Pathways
probe
affy
Pathways
probe
affy
written 17.7 years ago by
mike Ad.
▴ 30
3
votes
11
replies
2.6k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq
mixedmodels
baselineadjustement
limma
11 months ago
Anna
▴ 20
9
votes
11
replies
5.9k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 9 weeks ago by
shepherl
3.9k • written 2.3 years ago by
jon.klonowski
▴ 40
10
votes
11
replies
2.0k
views
tximport error: vroom
tximport
updated 6 months ago by
Abhishek
• 0 • written 7 months ago by
RLiu
▴ 40
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 7 months ago by
Michael Love
42k • written 7 months ago by
cm15245
• 0
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by
seeker
• 0
4
votes
11
replies
2.6k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 11 months ago by
Aung
• 0 • written 14 months ago by
pedro-marra
▴ 10
3
votes
11
replies
1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering
STD
DEG
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
alexia.brunel
• 0
1
vote
11
replies
3.6k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 6 months ago by
Manuel
• 0 • written 10 months ago by
Elham
• 0
0
votes
11
replies
2.9k
views
edgeR contrasts
edgeR
updated 9 months ago by
James W. MacDonald
65k • written 20 months ago by
ignadb
• 0
5
votes
11
replies
3.1k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
1
vote
10
replies
2.1k
views
Interprteting the phylogenomic profiles plot
syntenet
synteny
Network
written 18 months ago by
Alexandros
• 0
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 26 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
10
replies
839
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
6 months ago • updated 10 weeks ago
ScafioRuo
• 0
2
votes
10
replies
3.2k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 7 months ago by
Michael Love
42k • written 5.7 years ago by
andrebolerbarros
▴ 20
2
votes
10
replies
1.4k
views
can't open mghp.osn.xsede.org
GenomeInfoDbData
genomeinfodbdata
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
15753563659
▴ 50
0
votes
10
replies
2.3k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR
rna-seq
splice-variants
written 5.1 years ago by
saddamhusain77
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 4 weeks ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
3
votes
10
replies
2.8k
views
error in package GenVisR while installing
GenVisR
GenVis
updated 6 months ago by
zlskidmore
▴ 30 • written 22 months ago by
abhisikta
• 0
0
votes
10
replies
854
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware
ensembldb
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
cjag
• 0
4
votes
10
replies
1.8k
views
Archives prior to 3.15 gone
archive
bioconductor
updated 6 months ago by
shepherl
3.9k • written 20 months ago by
Florian Finkernagel
▴ 30
2
votes
10
replies
1.2k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago
rohitsatyam102
▴ 20
10
votes
10
replies
7.3k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 7 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
1
vote
10
replies
470
views
Obtaining pheno data from CEL files
GEO
affy
6 weeks ago • updated 5 weeks ago
Kurtis
• 0
3
votes
10
replies
421
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 5 days ago by
James W. MacDonald
65k • written 8 days ago by
Abbey
• 0
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
9 months ago
Luca
• 0
1
vote
9
replies
5.3k
views
how to control age and gender effect in expression data using DESeq2
deseq2
rnaseq
mirna-seq
differential gene expression
written 6.2 years ago by
klalit1803
• 0
4
votes
9
replies
1.4k
views
DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 9 months ago by
dbunis
▴ 10 • written 9 months ago by
nina.hahn
▴ 10
6
votes
9
replies
848
views
biomaRt has encountered an unknown server error.
biomaRt
host
useEnsembl
updated 3 months ago by
alexander3
• 0 • written 3 months ago by
Amparo
• 0
10
votes
9
replies
1.8k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 10 hours ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
9
replies
864
views
estimateDisp() error
edgeR
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
ASNbioinf
• 0
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 6 months ago by
blowfish
• 0 • written 6.5 years ago by
bharata1803
▴ 60
0
votes
9
replies
1.5k
views
Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin
DESeq2
updated 7 months ago by
yujin
▴ 10 • written 22 months ago by
Weiqian
▴ 10
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 8 months ago by
Novice_cam
• 0 • written 6.5 years ago by
knaxerova
▴ 10
2
votes
9
replies
1.8k
views
How to load fasta file with openPrimeR?
openPrimeR
written 3.2 years ago by
marongiu.luigi
• 0
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 2 hours ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
4
votes
9
replies
477
views
Memory errors using read.bismark?
dmrseq
bsseq
4 weeks ago • updated 8 days ago
Juan Higareda
• 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
10 months ago
Ndimensional
▴ 20
0
votes
9
replies
855
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
8 months ago
hayleyw
• 0
0
votes
9
replies
579
views
limma fo continous variables
limma
DEGseq
updated 11 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
mia
• 0
8
votes
9
replies
1.1k
views
All three of the sites where genomeinfodbdata R packages are stored appear to be down.
GenomeInfoDbData
9 months ago
15753563659
▴ 50
1,000 results • Page
2 of 20
Recent ...
Replies
Comment: error running enricher from clusterprofiler
by
Yael
• 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
Comment: Create protein sequences including variants from a VCF file
by
Yun
• 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization?
by
Daniel
• 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Votes
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Awards
• All
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
boczniak767
▴ 720
Popular Question
to
jmoon1194
• 0
Popular Question
to
mat.lesche
▴ 90
Popular Question
to
jordi.planells
• 0
Locations
• All
United States,
just now
Israel,
5 minutes ago
United States,
5 minutes ago
United States,
6 minutes ago
France,
10 minutes ago
Traffic: 897 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6